I would've done the following with regards to official Voyager Borg-themed episodes/story arcs (using the titles of existing, actual episodes):
Blood Fever (move the story to fairly early in Voyager's journey, and use it to set the stage for the rest of the series' Borg-related story arcs as per its 'B' plot/ending)
Unity (tie the story directly in with the aftermath of Descent, and set it fairly early in Voyager's journey but after their encounter with the Sakari, and use the story to give Janeway and the crew their first hint of exactly how powerful the Borg's technology is and plants in their minds the possibility of attempting to appropriate said technology for themselves in order to speed up their journey home)
Dark Frontier (set it chronologically fairly soon after the events of First Contact, with the crew finding out about those events and Janeway deciding to take advantage of
the Borg 'licking their wounds' to make a raid to try and steal their transwarp technology; introduce the character of SevenAnnika to the Voyager crew [with her having been introduced to the audience in general during FC), and plant in Janeway's mind the idea of rescuing her)
The Raven (move the story up so that it occurs between Dark Frontier and Scorpion, and use it to make Janeway officially decide that, if the ship encounters the Borg again, she's going to do everything she can to free Seven/Annika from the Collective)
Scorpion (introduce Species 8472, but do not make them so infinitely more powerful than the Borg, essentially making the conflict between the two species a stalemate until Voyager decides to get involved with the express purpose of Janeway freeing Seven/Annika and liberating her from the Collective)
Collective (tie the story in with the events surrounding Seven/Annika's liberation, and the events of Descent and Unity, set it fairly close to the end of the series, and end the episode with most, if not all, of the Borg children being successfully liberated and given berths aboard Voyager)
Endgame (utilize the presence of Seven/Annika and the Borg children aboard the ship to facilitate the infiltration of the Borg's transwarp hub, but make it clear that doing so is a source of conflict between the two Janeways, and use it to solidify the fact that Janeway's accepted Seven/Annika and the other ex-Borg into the ship's family)
This gives you a logical progression, story-wise, but without overusing or diluting the Borg or the threat they pose in any way.